If I understand correctly, these are multiple mdout files in sequence? The
mdout_analyzer.py program is more modern and flexible than the old perl
scripts and very good for multiple files. It stores and plots any and all
fields in the mdout file (including the instantaneous temperature).
It is worth mentioning that the program requires some additional 3rd party
python modules that you may not already have installed (gtk or something).
You can also write your own scripts using the modules in
"$AMBERHOME/bin/mdoutanalyzer" if you are somewhat adept with python.
Regards,
Brian
On Fri, Jun 27, 2014 at 10:37 AM, Valentina Romano <
valentina.romano.unibas.ch> wrote:
>
> Dear users
>
> I ran a MD simulation in parallel and I got 10 output files.
> (I got 10 mdcrd files: PknGAde_md01.mdcrd, PknGAde_md02.mdcrd etc.; 10
> .out files:PknGAde_md01.out, PknGAde_md02.out etc..)
>
> Now, I want to analyze results obtained.
> I mean, when I performed a 'non parallel' MD I used the process_mdout.perl
> script to perform to extract all properties. Now, each property is divided
> in 10 different file and I do not know I to use the process_mdout.perl
> script.
> If for instance I want to monitor the TEMP during the whole MD, I can do
> it?
>
> Thank you.
>
> Best,
> Valentina
>
>
>
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB
> Swiss Institute of Bioinformatics
> Klingelbergstrasse 61 | CH-4056 Basel |
>
> Phone: +41 61 267 15 80
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--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for
Integrative Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
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Received on Fri Jun 27 2014 - 08:30:02 PDT
